Monday, May 07, 2007

Theme: The Three Domain Hypothesis

This is a series of postings that describe the Three Domain Hypothesis. The Three Domain Hypothesis is the idea that life is divided into three domains—bacteria, archaebacteria, and eukaryotes—and that the archaebacteria and eukaryotes share a common ancestor. An example of this tree of life is shown on the Dept. of Energy (USA) Joint Genome Initiative website [JGI Microbial Genomes] (left).

11 comments
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You've mentioned before that the Three Domain Hypothesis has been abandoned; is this a premature statement? It is still widely used in the literature, even in the top tier journals (Nature, Science, PNAS). I don't necessarily disagree with you, but the rest of the universe hasn't seemed to catch on.

Seriously, Woese did such a good job of selling the Three Domain Hypothesis that most people have just accepted it as fact without checking to see if it's holding up in the molecular evolution literature.

Once a new fad gets promulgated it's very hard to convince people to stop believing.

I hate to be the one to break it to you but there are lots and lots of things in Nature, Science, and PNAS that aren't true. Sorry. :-)

This is all fascinating reading, and I thank you again for (re)posting it. I'd like to repost my comment-question from last time:

If the deep phylogeny of cells/organisms/genomes is, then, unknowable, what CAN we say? Eukarya seems unquestionably monophyletic (leaving mitochondria and plastids aside, of course) and so we are left with a huge, diverse, possibly paraphyletic (but we'll never know) and possibly even polyphyletic??? (but we'll never know) Domain Monera? This is rather unsatisfying, but if that is the situation, so be it.

If the deep phylogeny of cells/organisms/genomes is, then, unknowable, what CAN we say?Eukarya seems unquestionably monophyletic (leaving mitochondria and plastids aside, of course) and so we are left with a huge, diverse, possibly paraphyletic (but we'll never know) and possibly even polyphyletic??? (but we'll never know) Domain Monera?This is rather unsatisfying, but if that is the situation, so be it.

It's worse than you imagine.

At the deepest level, you can't say that eukaryotes are any more monophyletic than bacteria. That's the whole point. The first identifiable eukaryotic species emeged from the mix several billion years ago but before that the lineages are so intertwined that there's no point in distinguishing eukaryotes and prokaryotes.

Surely you are not suggesting that extant eukaryotes are not monophyletic. You mean that the prokaryotic ancestors of extant eukaryotes were part of the whole horizontally-gene-transferring mess. Right?

viruses are...special. I was first taught at school that they were bits of 'lost' DNA that had escaped from things and managed to somehow surround themselves with proteins. Recently though, I'e come across the idea that virus's are 'escaped' DNA that have got out and found they can live a life of their own.

I'm currently working on bacteriophages, which in some cases can carry bit of DNA from bacteria, making them...related? Viruses are, thinking about it, another reason this hypothesis is starting to crumble.

to Cameron: The reason this is still used is probably because it's a very useful model, despite probably not being wonderfully correct.

It is very difficult to overturn the pioneering significance of Woese's discovery of the Archaea. Admittedly he's a great self-promotor and who can condemn this given how the establishment resisted his Tree-Thinking as applied to what came to be called the microbosphere? [see for overview - Morell, V. (1997) Microbiology's scarred revolutionary. Science 276:699-702]

There is much more at stake in his manifesto and in how Woese turned microbiology back to face the reality of microbial diversity. I rate these essays as amongst those great's one should read at least once/year :-)

Woese, C. R. and N. Goldenfield (2009) How the microbial world saved evolution from the Scylla of Molecular Biology and the Charybdis of the Modern Synthesis. Microbiology and Molecular Biology Reviews 73:14-21.

Woese, C. R. (2004) A new biology for a new century. Microbiology and Molecular Biology Reviews 68:173-186.

Laurence A. Moran

Larry Moran is a Professor in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.